Across 13 protein language models and 15 downstream tasks, the last layer is rarely the best source of embeddings; intermediate layers work better, and the best layer is set by dataset structure rather than by the task alone.
Comparative assessment of protein large language models for enzyme commission number prediction.BMC bioinfor- matics, 26(1):68, 2025
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Task- and dataset-specific information in protein language models
Across 13 protein language models and 15 downstream tasks, the last layer is rarely the best source of embeddings; intermediate layers work better, and the best layer is set by dataset structure rather than by the task alone.